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Yorodumi- PDB-4hp2: Invariom refinement of a new dimeric monoclinic 2 solvate of thio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hp2 | ||||||
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Title | Invariom refinement of a new dimeric monoclinic 2 solvate of thiostrepton at 0.64 angstrom resolution | ||||||
Components | Thiostrepton | ||||||
Keywords | ANTIBIOTIC / THIOPEPTIDE / ANTIBACTERIAL / THIAZOLE / THIAZOLINE / OXAZOLE / RIBOSOME / TRANSLATION INHIBITION | ||||||
Function / homology | Thiazolylpeptide-type bacteriocin precursor / defense response to bacterium / extracellular region / THIOSTREPTON / DIMETHYLFORMAMIDE / diethyl ether / Thiostrepton Function and homology information | ||||||
Biological species | Streptomyces azureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SHELXS/DIRECT-METHODS / Resolution: 0.64 Å | ||||||
Authors | Proepper, K. / Holstein, J.J. / Huebschle, C.B. / Bond, C.S. / Dittrich, B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Invariom refinement of a new monoclinic solvate of thiostrepton at 0.64 angstrom resolution. Authors: Propper, K. / Holstein, J.J. / Hubschle, C.B. / Bond, C.S. / Dittrich, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hp2.cif.gz | 37.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hp2.ent.gz | 34 KB | Display | PDB format |
PDBx/mmJSON format | 4hp2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hp2_validation.pdf.gz | 449.7 KB | Display | wwPDB validaton report |
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Full document | 4hp2_full_validation.pdf.gz | 461.6 KB | Display | |
Data in XML | 4hp2_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 4hp2_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/4hp2 ftp://data.pdbj.org/pub/pdb/validation_reports/hp/4hp2 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Type: Thiopeptide / Class: Antibiotic / Mass: 1805.985 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 56-72 / Source method: isolated from a natural source Details: Thiostrepton is a hetrocyclic thiopeptide belonging to the thiocillin family, consisting of four thiazole, one thiozoline and one piperideine rings. A modified quinoline linked to main-chain ...Details: Thiostrepton is a hetrocyclic thiopeptide belonging to the thiocillin family, consisting of four thiazole, one thiozoline and one piperideine rings. A modified quinoline linked to main-chain residue 1 and side-chain of residue 12. Post translational maturation of thiazole and oxazole containing antibiotics involves the enzymic condensation of a Cys or Ser with the alpha-carbonyl of the preceding amino acid to form a thioether or ether bond, then dehydration to form a double bond with the alpha-amino nitrogen. Thiazoline or oxazoline ring are dehydrogenated to form thiazole or oxazole rings. the pyridinyl involves the cross-linking of a Ser and a Cys-Ser pair usually separated by 7 or 8 residues along the peptide chain. The Ser residues are dehydrated to didehydroalanines, then bonded between their beta carbons. The alpha carbonyl of the Cys condenses with alpha carbon of the first Ser to form a pyridinyl ring. The ring may be mutiply dehydrogenated to form a pyridine ring with loss of the amino nitrogen of the first Ser. The amidation of Ser-17 probably does not occur by the same mechanism, oxidative cleavage of glycine, as in eukaryotes. Source: (natural) Streptomyces azureus (bacteria) / Strain: MST-AS4632 / References: UniProt: P0C8P8, THIOSTREPTON #2: Chemical | ChemComp-DMF / #3: Chemical | ChemComp-ETZ / #4: Water | ChemComp-HOH / | Compound details | THIOSTREPTON IS A MEMBER OF A SULPHUR-RICH HETEROCYCLIC PEPTIDES CLASS. ALL SHARE A MACROCYLIC ...THIOSTREPT | Sequence details | A MODIFIED QUINOLINE QUA LINKED TO THE MAIN-CHAIN OF ILE 2 AND THE SIDE-CHAIN OF THR 13. BB9 14 ...A MODIFIED QUINOLINE QUA LINKED TO THE MAIN-CHAIN OF ILE 2 AND THE SIDE-CHAIN OF THR 13. BB9 14 INCLUDES HYDROGEN ATOM H6, THE DEHYDROPIP | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.48 Å3/Da / Density % sol: 16.88 % |
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Crystal grow | Method: vapor diffusion / pH: 7 Details: DIMETHYLFORMAMID, DIETHYLETHER, pH 7.00, VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.65 |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.65 Å / Relative weight: 1 |
Reflection | Resolution: 0.64→50 Å / Num. obs: 72903 / % possible obs: 91 % / Redundancy: 3.61 % / Rmerge(I) obs: 0.0505 / Net I/σ(I): 16.88 |
Reflection shell | Resolution: 0.64→0.65 Å / Redundancy: 0.67 % / Rmerge(I) obs: 0.1457 / Mean I/σ(I) obs: 3.46 / % possible all: 46.4 |
-Processing
Software |
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Refinement | Method to determine structure: SHELXS/DIRECT-METHODS / Resolution: 0.64→50 Å / Cross valid method: LEAST SQUARES / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 0.64→50 Å
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